The Wandering Maelstrom V2
by Vanex
Summary: The Fourth Shinobi War ended with a shocking twist. A couple thought to be dead returns and takes over the Five Great Shinobi Countries. The world is trapped under the reign of the Fire Emperor and the Fire Empress. But, who is this strange wanderer, this Maelstrom, that is dead set on ending their reign? Featuring my OC, Sora. Main Pairing: Naruto x ?
1. Arc 1 Chapter 1

**Vanex: _Hello all! This is the rewrite of The Wandering Maelstrom. I'm going to go about this differently than before, and with a different love interest planned. Originally, it was to be an OC, one Sora Nakamura. She will still be in this story, and she will still travel with the regenerated Naruto. However, there will be no romance between the two. Instead, I have something else planned for the two of them._**

_**Also, DO NOT read A Lost Outcast. It ties into the original Wandering Maelstrom, not this story. An updated version will be released in this story.**_

_**Finally, I apologize for getting this chapter out days later than I had planned, but like I said in Impression, I have a busy life. I may have let out the small detail that not only am I moving into a new house, I'm renovating said house.**_

_**Let's get started.**_

**Disclaimer: I do not own Naruto or Doctor Who, nor do I make any profit on this, whatsoever.**

"Normal Talking"

"_Dreams/Flashbacks"_

"**Demon Talking"**

*Scene Change*

**Arc 1: The Birth of the Maelstrom**

**Chapter 1**

Naruto lets out a laugh. Madara Uchiha, the greatest threat to the world in quite some time, has been defeated. Madara had been planning to use the Demonic Statue of the Outer Path to recreate the original Jūbi, by having the statue absorb the nine Tailed Beasts. He would then use its power to make the world the way he wants it to be.

Madara had succeeded in recreating the Jūbi, but before he could place himself in control of it, it disappeared. Everyone had been surprised at this event, but none more so than Madara. Naruto, who survived the extraction of Kurama, confronted Madara. He distracted the Uchiha, giving Sasuke the chance to attack Madara with a technique given to him by the First Hokage.

The technique was designed to affect the part of Madara's body that contained Hashirama's cells. In fact, the technique's purpose was to destroy the cells. Unfortunately for Madara, the portion of his body that had Hashirama's cells was in the same area as his heart. Death was instantaneous.

Naruto falls to his knees, breathing heavily. Sakura runs over to him. "Naruto!"

He smiles at her. "Hey, Sakura."

"What's wrong with him?" asks Sasuke.

Sakura does a scan of Naruto's body and her eyes widen. "Naruto, you're body isn't adjusting to the loss of the Kyūbi. You're dying."

"I know, Sakura. I can feel it. Help me up."

"But, Naruto..."

"I said help me up, Sakura! Please." Sakura hesitates for a few moments, before nodding and helping Naruto to his feet. Naruto looks at his hands. "So, in the end, all that drive to become Hokage was for nothing. All my speeches about not dying until I become Hokage were just delusions in the end." He turns to see the other surviving ninja from the Shinobi Alliance and smiles sadly. He looks at his hands again and pauses. He feels something in his right hand, and when he looks at it, the center of his palm momentarily glows with a golden-orange light. "What the?"

Suddenly, Orochimaru lets out a scream of pain. Everyone looks at him to see him on his knees, clutching his neck. A few seconds later he stands back up, with a blank look on his face. He makes a handsign, and the first three Hokages are sent back to death. He then makes another handsign, and the Fourth Hokage just melts, like an Earth Shadow Clone.

"Well done with destroying Madara, Naruto and Sasuke."

Everyone turns to see a shocking sight. Minato Namikaze is standing there, along with Kushina Uzumaki, and a girl who looks like a younger Kushina. What's shocking about Minato and Kushina is that they don't look reanimated. They are definitely alive. "Dad," asks Naruto, "how are you and Mom alive? What's going on?"

Minato smirks. "That's easy, Naruto. We're alive because we never died."

"What?" Naruto feels something in his left hand, and looks to see the center of his left palm momentarily glow with the same golden-orange light that his right palm had. He shakes his head. He needs to focus on the immediate problem, not on what's going on with him. He looks back at his father. "What do you mean, you never died?"

"I mean exactly that. We didn't die the night of the Kyūbi attack. We both survived."

"But, I talked with those imprints you left behind!"

Minato nods. "Yes, but it doesn't mean that we have to be dead for them to work. They did their part, driving you to get strong enough to defeat Madara."

"So it was all a lie?" He turns to look at his mother. "Was everything you told me a lie?"

Kushina shakes her head. "No, not all of it. Most of what I told you was true. I was the previous Jinchūriki of the Kyūbi, and I did honestly tell you how your father and I met."

Naruto grimaces in pain. He feels the same strange feeling as before, and looks at his hands to see the strange light again, only it's spread to cover the entire palm on both hands. He can feel a strange energy starting to flow through him. What the heck is going on? He shakes his head. "Why did you lie to me?"

"We lied so you would push yourself to be strong enough to defeat Madara," says Minato. "He was the last threat to our plans."

"What plans?"

Minato smirks. "Our plans to take control of the Five Great Shinobi Countries of course."

This puts all the ninja present on edge. Sasuke raises an eyebrow. "And how exactly do you plan on taking over, with this many ninja in your way?"

Minato merely smirks, before making a handsign. Most of the ninja scream in pain as they clutch at their necks. A few seconds later, they stop, only now they have blank looks on their face. Naruto can see something glowing on the back of Sakura's neck. "It's a seal."

"That's right," says Minato. "It's a loyalty seal. Every ninja that I managed to secretly put the seal on, is now under my control. Granted, not every ninja has the seal on them. But most of them are, including Orochimaru, as you can see. He was the first one I marked, back when I was the active Hokage."

"How did you mark them all without anyone seeing you?"

"By putting the seal on any witnesses. I then order them to forget that they saw me, and they do. It took a great deal of time to mark them all. Soon, the rest will be marked, except for you, Naruto."

"Why am I an exception?"

"You're our son. You'll be standing at our side, along with your younger sister, Mito." He gestures to the girl that is with them. The girl doesn't say anything. She just stares at Naruto. Minato doesn't notice. "What did you expect us to do with you?"

"Considering the life you left me to, I wouldn't be surprised if you wanted me to die."

Minato sighs. "Yes, things don't always go as planned. Konoha was really supposed to treat you like a hero." He shrugs. "No matter. You still turned out well."

Kushina smiles. "Join us, Naruto. Take your place at our side, as the prince of this new world."

Naruto stand there, silently, for a few moments. Then, he scowls. "Join you? Join this mad world you're creating? A world in which everyone is enslaved is no world I want to live in! I would rather die before ever joining you!" He feels another jolt of pain. "And that is exactly what is going to happen."

"What are you talking about?" asks Minato.

"My lord, his body is failing to adjust to the loss of the Kyūbi," says the enslaved Sakura. "Lord Naruto is dying."

The eyes of both Minato and Kushina widen in shock. "But, that wasn't supposed to happen!" proclaims Minato. "Your body was supposed to adjust, just as your mother's did!"

"But I had help, Minato!" says Kushina. "We had Tsunade with me to help my body adjust!"

Naruto lets out a yell as he feels another jolt of pain. He can feel the strange energy flowing more intensely through him and he looks at his hands to see the glow appear again, only now it has spread to cover the back of his hands. This time, everyone notices the glow. "What's going on?" asks Minato. No one knows, especially not Naruto. Minato starts to move forward towards Naruto, when he is interrupted.

"Amaterasu!" A wall of black flames appears, preventing Minato from reaching Naruto. Sasuke grabs Naruto's arm. "Come on, Naruto!" Sasuke pulls Naruto away.

"Stop him!" yells Minato.

The ninja, that are on the same side of the flames as Naruto and Sasuke, move to capture them, but three people suddenly appear in front of the duo. They were three of the five Kage, the only two missing being Tsunade and Gaara.

Naruto notices this. "Where are Granny Tsunade and Gaara?"

"Tsunade's dead, Naruto," says the Raikage. "She gave her life to save ours."

Naruto's eyes widen, before another jolt of pain passes through his body. This time, the glow has encompassed both hands entirely. "What's happening to me?"

The Raikage gives the duo a look. "Sasuke, get Naruto out of here. We'll hold them off." He then looks at all the ninja. "Anyone who isn't under the control of the Fourth Hokage, we order you to get out of here. Do what you can to escape."

Sasuke quickly leaves with the dying Naruto. Minato tosses one of his special kunai over the flames, and teleports both himself and Kushina to the other side. Minato looks at his wife. "Go get Naruto. I'll deal with these three."

Kushina nods and heads after Sasuke and Naruto. The Raikage tries to intervene, but Minato uses another kunai to teleport right in front of him with a Rasengan ready.

*With Naruto and Sasuke*

Sasuke is carrying Naruto on his back as they head through a forest. They don't get far before a chakra chain hits Sasuke, causing him to drop Naruto. Sasuke lands on a branch and can only watch as Naruto falls to the forest floor, and starts to roll down the hill the forest is on. Sasuke then blocks another chain with his sword, as Kushina lands on the branch across from him. He glares at Kushina. "So, you're Naruto's mother? You disgust me, abandoning him when he was young."

Kushina scoffs. "You're one to talk, considering you abandoned him for your precious revenge."

Sasuke shrugs. "That is true, but you were his family, the one thing he wanted more than anything else, even more than his dream of being Hokage. If there was one thing that he and I could truly agree on, it was how precious a family was."

"And he will have his family. He will be with us, and you won't stop this, Sasuke." Kushina shakes her head. "It's a shame that I have to defeat my own godson to get to him."

This surprises Sasuke. "What?"

"You didn't know? Your mother and I were close friends. Honestly, I'm surprised that Mikoto managed to convince Fugaku to name me your godmother."

Sasuke scowls. "So, you not only abandon your own son, you abandoned me as well. And you expect me to just hand over Naruto to you?"

Kushina shrugs. "You haven't been his friend for years, why do you care what happens to him?"

"Because even I won't abandon him now, at the end of his life."

"He won't die. I won't let him." Kushina draws a sword. "I've been trained by some of the best sword-masters out there. Do you really think you can beat me?"

Sasuke smirks. "We'll see." The two charge at each other, and their swords clash.

*With Naruto*

Naruto finally comes to a stop at the bottom of the hill. He can feel the added pain from a couple of trees he hit on the way down, along with the pain he is already feeling. He manages to stand again. The strange energy feels even more intense now. He looks at his hands, as golden-orange energy starts leaking from them. "What is this energy? It's not from Kurama."

He suddenly notices the same energy in his vision, and realizes that his head is also leaking the same energy. "Whatever it is, I can't stop it! It's trying to push itself out of my body! I'm going to explode!"

He can't hold it back anymore. He extends his arms as the energy shoots out of his head and hands at an intense rate.

*Back with Sasuke*

Sasuke and Kushina both see a golden-orange light coming from down the hill. Sasuke's eyes widen. "That's where Naruto fell!" Both he and Kushina look at each other, before disengaging and charging down the hill, determined to reach Naruto before the other one could.

*Back with Naruto*

The energy fades. He stumbles and realizes that his jacket has suddenly become tight. He struggles with the zipper, but manages to unzip the jacket. "That's better." He feels dizzy. "Oh, my head. What's happening to me?" He hiccups, and a wisp of golden-orange energy comes out from his mouth. "What the heck?" His mind is foggy, but he does remember that he needs to run from something. He turns and runs further into the forest, intent on escaping from whatever it is that he can't remember.

Half a minute after he leaves, Sasuke and Kushina arrive. Kushina is pissed. "Naruto's gone! It's your fault this has happened!" She attacks Sasuke again.

Sasuke defends himself. "Me? You're the one who caused me to drop him!" Sasuke jumps back from Kushina. "Amaterasu!" He creates another wall of black flames, blocking Kushina from reaching him. He turns and runs, knowing that staying here was pointless now. Naruto was long gone.

*With Naruto*

He emerges from the forest to find himself at a village. "Wait, I know this place. This is Amaru's village!" His dizziness hits him again as he stumbles into the village.

A familiar girl sees him and rushes over to him. "Are you okay, stranger? You look like you're about to fall over!"

He looks at her and his mind clears. "Amaru, you need to hide me!"

Amaru is confused. "Do I know you?"

"Please, Amaru! You need to..." He trails off as he falls unconscious.

**Vanex:_ So, what do you think of the changes? Let me know. Oh, and before you ask me what happened to Gaara, I'll tell you now that it will be revealed in the future. See you all next time!_**


	2. Arc 1 Chapter 2

**Vanex: _Hello all! Sorry it took so long to release this chapter. __I allowed myself to get sidetracked, with different games, __the holidays, and the book I'm writing. Updates are going to be sporadic from now on, cause I'll be focusing more attention on the book, cause getting an actual book written and published is more awesome. No offense to fan fiction._**

**_N__ext important note is one I thought I said, but I can't seem to find that I said it, so I'll say it here. At this time, I'm NOT accepting any new challenges or requests. I want to work on my own stories first. So, I better not get anymore requests in the PM, because I will ignore them, and even delete them if a requester keeps bugging me about his or her request, __possibly even blocking the requester__. __(This has already happened once.)__ Sorry, but I just simply don't have the time. Real life always takes priority._**

**_One last thing, __I will remind you all that this story was created before Kaguya's resurrection and the reveal of the true circumstances of the birth of the J__ū__bi.__ Thus, this story's version of events will conflict with canon events. You won't see the changes in this chapter, or this story arc for that matter, but they will pop up in later arcs. Now then, let's get to it._**

**Disclaimer: I do not own Naruto or Doctor Who, nor do I make any profit on this, whatsoever.**

"Normal Talking"

"_Dreams/Flashbacks"_

"**Demon Talking"**

*Scene Change*

**Arc 1: The Birth of the Maelstrom**

**Chapter 2**

*One day later*

Minato sighs as he looks out over the Fire Capital. His rise to power hasn't gone exactly to plan. He managed to kill the Raikage and the Tsuchikage, but the Mizukage escaped. The five Daimyō have disappeared, having been spirited away by the Kazekage during the fight. Worst of all, Naruto had rejected them and then disappeared. How could he do so? Couldn't he see that the only way to prevent future wars from happening is to take control? Couldn't he see how impossible true peace is?

There are still two mysteries about the whole thing. There is the strange energy that engulfed Naruto. Minato has never seen anything like that before. It didn't have anything to do with the Kyūbi, as the beast had been extracted from Naruto. The second mystery is the disappearance of the Jūbi. He has no idea why it just vanished like that. He will have to be on his guard, in case it ever returned.

A knock on the door interrupts his thoughts. "Come in."

The door opens and Kakashi walks in. "You called for me, Sensei?"

"Yes, Kakashi. I want you to try to track down where Naruto has gone. Kushina and I want to know for certain whether he is alive or dead. If he is dead, then bring back his corpse, so he can be given a proper funeral. If he is alive, bring him back using any means necessary, except for killing him."

Kakashi nods. "I understand."

*In Amaru's village*

Amaru sighs as she finishes some paperwork at her clinic. Today has been a quiet day with no patients, except for one. She gets up and heads over to the occupied bed. The young man laying on the bed is a complete mystery to her. He knows her by name, while she is absolutely sure she's never seen this man before. However, she'd recognize his clothes anywhere. Only one ninja ever wore clothes like that. But, this man looks nothing like Naruto Uzumaki.

Her medical scan made things more puzzling. His body showed signs of massive internal damage, specifically to his chakra coils. However, there was a bizarre energy flowing throughout his body. Not only was it healing the damage, it was changing everything inside him. The old organs were being changed into new versions of them, and his blood was also changing, most likely to be compatible with the new versions of the organs. The chakra coils were also being affected, shrinking to accommodate less chakra than before, signifying that he had somehow lost a portion of his power. The chakra itself was in a state of flux, which would make it impossible for a Hyūga to identify him.

All of this makes her consider an important question. Are these changes only internal, or are they also external? On the outside, his body shows no signs of any damage, except for tears in his clothes. It's likely this process changed his external appearance first, as well as healing the main damage done to him. She had only been lucky to determine that the damage had even existed because there were still internal signs of the damage, but those signs were quickly disappearing. Most likely, the internal portion of this process takes longer, which is probably why he is unconscious. Any extra strain would probably disrupt the change.

Amaru shakes her head. What kind of healing process is this? She has never seen anything like this before. Hopefully, she'll be able to get answers from him, when he wakes up. She has doubts to getting answers, as his brain is also being affected by the process. He might not even have a stable mind upon awakening, which is why Amaru has restrained him to the bed.

Amaru sighs again, as her thoughts shift to everything going on outside. She looks out her window and watches as some ninja walk past her clinic, ninja enforcing the will of their new Emperor and Empress. There are dark days ahead for the world, and all she can do is hope that she and her fellow villagers will be able to survive past those days.

*Where Naruto's regeneration occurred*

Kakashi, along with Kiba, Hinata, and Shino, are searching for any clues to what happened to Naruto. "Any of you find anything, yet?"

Shino nods. "My bugs are acting strange, only when I stand in this particular spot. Something happened here."

"There's an odd scent in the air," says Kiba. "It's faint, over a day old. I don't know what to make of it. It's concentrated in the same spot that Shino mentioned, and there's a second scent. It's also in the same spot, but there is a trail heading away from it, in that direction."

"Look at this," says Kakashi, who is kneeling on the ground. "There are footprints, heading off in the same direction." He nods. "This is our best lead. We'll follow the scent and footprints. Hopefully, we'll find Naruto."

The four start to turn to leave the area, but Hinata suddenly stops. The entire time, she has been scanning the area with her Byakugan. For a second, she sees someone nearby, but the signature vanishes quickly. "What the?"

"What's wrong?" asks Shino.

"I thought I saw someone, but there's nothing out there now. It may have been a figment of my imagination, or someone is able to cloak themselves from the Byakugan, which should be impossible."

Kakashi is immediately on alert. "We'll have to proceed carefully, then. Assume that we are being followed by someone. Don't drop your guard."

The other three nod and follow him away from the site. Not long after that, a young woman arrives. She is dressed in an all black ensemble, consisting of a shirt, pants, combat boots, armbands, and a long coat. The woman brushes back her brown hair, as she looks around. "Well, well, you continue to surprise me, Naruto. No one in your clan has been able to use a regeneration in a very long time, not since your ancestor, the First Uzukage."

The woman starts walking in the direction of the village that Kakashi's team is heading for. She thinks back to the first time she met Naruto. "I could sense that there was something about you, something that makes you different from everyone else, including that damn sage and his even more detestable mother. I look forward to seeing where your path will take you next." She laughs as she disappears into the forest.

*In Amaru's clinic*

The young man lets out a groan, as he awakens. "Where am I?" He notices that he is restrained, and struggles, trying to break free. "What's going on?"

Amaru comes running up to the bed. "Please, calm down. You're in my clinic. You're safe. The restraints are only for your own protection."

The man calms down, as he stares at Amaru. "Hold on, I know you." A grin appears on his face. "You're Amaru! I knew you looked familiar! How are you doing?"

"You know me?"

"Of course I know you! Why wouldn't I know you? And when are you going to take these stupid restraints off?"

"But, I don't know who you are."

The man is confused. "How do you not know who I am? After what we went through with that Sora no Kuni incident? How could you forget me, Naruto Uzumaki?"

Amaru's eyes widen. "You really are Naruto?"

"Of course I am! What's wrong?"

Amaru runs off, and then comes back with a hand mirror. "See for yourself." She holds up the mirror in front of Naruto's face. Naruto's eyes widen at seeing his reflection.

"What the heck? That's not me! What's going on?"

Amaru puts down the mirror and removes the restraints. "I was hoping you would be able to tell me. Your body is full of a strange energy that is healing and changing you. I've never seen anything like it. What happened? I noticed signs that something had happened that damaged your chakra coils. Don't worry, the coils have healed, but they've shrunk, which means you have less chakra."

Naruto's eyes widen as he realizes why. "Kurama was extracted from my body."

"Kurama?" 

"Sorry. I'm talking about the Nine-Tailed Fox."

Amaru's eyes widen as she realizes what that means. "But, you should be dead! From what I've researched about Jinchūriki, the extraction of the Tailed Beast means certain death!"

Naruto shrugs. "I honestly have no idea why I'm still alive, or why I've changed like this. In fact, it's hard to really think of anything." He puts his hand to his head. "My mind is so jumbled, that I'm having trouble thinking."

Amaru nods. "It's the energy's doing. Like I said, it's healing and changing you. All your organs are being affected, including your brain. Your body is adapting to the changes, so it's likely your mind will too, in time. For now, I'd like you to stay here, and give yourself time to finish healing."

"Can I get some new clothes, first? My old ones don't fit me anymore."

"We can worry about buying you some new clothes after you recover. But, I do have a friend that's about your size. I don't think he'll have any problems loaning you some clothes, until you can get some of your own." 

Naruto nods, before laying back on the bed. "Normally, I would be against this, but since I'm having trouble just thinking, I'll put up with this. The sleep with be good for me." He pauses for a moment. "One last thing. Tell no one I'm here, regardless of who that person is."

"Why?"

"I don't remember. I may be able to tell you in a few hours, if my head clears up."

Amaru nods. "I understand. Sleep well, Naruto." She leaves the room, heading off to contact her friend.

**Vanex: _There we go. Chapter done. See you all next time!_**


End file.
